Hi, I'm Keshav Ramji. I am a rising sophomore at Arlington High School in Lagrangeville, New York. My interest in synthetic biology and biotechnology came from my 9th grade biology class, during a unit on genetic engineering, which really enthralled me. I hope to one day pursue a career in data science, biostatistics/bioinformatics, or computer science. I have participated in our district science fair for the last 8 years, and participated in the county wide science fair for the last 5 years. I was also a Broadcom Masters nominee in 6th grade. I play the mridangam(Indian classical drum), and the viola. I am also a USTA tennis player in the Eastern Section and play singles on our school's varsity team. I love sports analytics and bracket challenges, and enjoy watching basketball. I am looking forward to learning new techniques and conducting some interesting research during these 3 weeks!
Quorum Sensing Using Synthetic Bacteria for Detection of CancerousTumors I. Purpose
Cancer is obviously a major issue that our world is facing today. While the mortality rate is slowly decreasing, cancer is not being detected in its early stages when tumors are easier to eliminate. The survival rate in lower stage tumors is drastically higher than in late stage tumors. For example, the survival rate in stage 2 breast cancer is 92%, while the survival rate for stage 4 breast cancer drops drastically to 21%. The reason why cancerous tumors are not being detected in early stages are that they are too expensive for many people to afford. The scanners used are seldom found in the United States, and therefore they are also not accessible to most patients. This issue is important since more people will survival through early detection. The proposed design will solve this issue by making tumor detection more affordable and accessible by optimizing the use of CT and MRI scans which are currently under-utilized.
II. Competing Technologies
The major method of cancer detection is the PET (Positron Emission Tomography) scan. During this scan, the patient is injected with a glucose solution, which contains a minimal amount of radioactive material. Since cancer cells use up more glucose, the PET scan checks for the amount of glucose intake by the cells in the region. The rate at which the glucose is absorbed by tumors is indicative of the stage of the tumor: the faster the rate of glucose absorption, the higher the stage of the tumor. While they are effective in detecting tumors, too much radioactive material can be harmful, and they are also very expensive, often costing nearly $10,000 or more.
III. The Design
Pseudomonas Aeruginosa is a type of gram negative bacteria, which uses quorum sensing for swarm motility, or translocation as a swarm. This bacterium is highly pathogenic and parasitic, and this could lead to major problems. However, with their swarm motility function, it is the perfect bacteria to use for redesigning a chassis. The chassis will be redesigned using the top down method, removing genes repeatedly to find the genes required for to bacteria to survive. Through this process, the parasitic genes will be removed, effectively making the bacteria non-pathogenic. The parasitic genes will be discarded. The genes required for survival, along with the gene for producing receptors for N-AHL (N-acyl Homoserine Lactones, a common signal molecule for gram negative bacteria), a gene for producing N-AHL signal molecules, a gene that allows for binary fission as an asexual reproduction method (this will be in the group of gene required for survival, the GFP (Green Fluorescent Protein) gene, a gene for production of Antigen (Ag) Specific Receptors, and a gene for producing receptors for the major hormone in the organ that is being examined (this is patient-specific and varies from case-to-case).
The genes will be used by a DNA synthesizer to create a genetic code, which will be placed in a synthetic cell. It is also required that antigens will need to be placed on the synthetic bacteria once created since when the bacteria enter the body, the immune system will attack them as foreign cells due to them not having the body’s antigens. Therefore, a blood sample will need to be taken from the patient to extract antigens from red blood cells, which is a very common procedure. The extracted antigen will then bind to the Antigen (Ag) specific receptors on the cell surface.
The Pseudomonas Aeruginosa reproduces by Binary Fission, and therefore by moving the genes for survival of these bacteria, this includes the gene for binary fission, as reproduction is one of the key tenants of life. The rate of reproduction for binary fission is around 20 minutes, so in 12 hours, this can produce about 137.5 billion bacteria. After the bacteria reproduce for about 18 hours, a bacteriostatic agent will be used to stop the synthetic bacteria from reproducing, but without killing them (the specific bacteriostatic agent will have to be found using trial and error, because there is no specific bacteriostatic agent which will work for pseudomonas aeruginosa).
While the bacteriostatic agent is added, a bioinformatics database will be used to compare the genetic codes of the synthetic bacteria with the original code that was created to check for mutations. This is imperative to ensure that mutated bacteria do not enter the body during the tumor detection phase. Pseudomonas Aeruginosa has a high rate of mutation, nearly 67%, so many bacteria will need to be killed off to prevent mutated bacteria from entering the body. Then the bacteriostatic agent will be removed and the non-mutated bacteria will be allowed to reproduce. After many of these cycles, and after approximately 1 trillion bacteria are produced, the bacteria will be injected into the organ where symptoms of cancer are present using a syringe.
In the organ, the bacteria will search for the tumor using quorum sensing for swarm motility (translocation). The synthetic bacteria were given the gene for receptors of a major hormone in the specific organ since changes in major hormone levels can indicate the presence of cancer cells. While the bacteria move through the organ, if they detect a tumor, the gene for GFP will be turned on and the tumor region will fluoresce green. This will allow humans in the outside world to be able to find the tumor location using a MRI or CT scan. If a tumor is not present in the organ, there will not be any green fluorescent color.
While there may not be any cancer in this organ, this does not guarantee that the patient is 100% cancer-free, as the tumor could be located just outside the organ, while the bacteria may not detect this. Therefore, this entire procedure may have to occur multiple times in different locations to make sure that the patient is cancer-free overall. However, the cost of doing many of these tests will still be far less than doing a PET scan.
Synthetic Design Process Flow
Quorum Sensing and Tumor Detection Flow Chart
IV. Expected Results
When the design is working perfectly, all the genes aforementioned will be present and be activated in the minimal bacterial cell, the bacteriostatic agent will completely stop reproduction without killing the bacteria, the bioinformatics database will clearly differentiate between mutated bacteria and non-mutated bacteria, the bacteria will be able to use quorum sensing to move through the organ, and GFP will be activated in the presence of a tumor (if it so exists). The logic switch used will be a buffer gate, with 0 to 0 and 1 to 1 correspondence.
Truth Table
V. Advantages
This design reduces the cost of cancer and tumor detection by nearly 5 times. While there are only a grand total of 62 PET scanner locations in the country, there are thousands of MRI locations, and thousands more CT scanner locations, as these are available at a large amount of hospitals across the country. Two of the five most populous states, New York and Illinois, do not even have PET scanner locations across the entire state. That amounts to over 32 million people who have limited access to cancer detection.
This design is worth funding since it is a solution that makes cancer detection more cost effective and more accessible. This design can save millions of lives of people who are dying of cancer because it is not being detected early enough, which ultimately traces back to affordability.
VI. Potential Problems
If there is a genetic engineering error, this could end up introducing an extremely pathogenic organism into a human, and this would be a very dangerous scenario. Likewise, if the bioinformatics database check is not done to perfection, this could introduce mutated bacteria into the body, and the mutations can be harmful. The bacteriostatic agents must work perfectly to ensure that the bacteria stop reproducing during the bioinformatics database check, while not killing the bacteria. The experiment will need to take place in a very controlled lab environment, to prevent the Pseudomonas Aeruginosa (before it is genetically modified) to infect employees. Also, it is imperative that the mutated synthetic bacteria do not escape the lab environment and cause havoc as these mutations are dangerous. With this design, the rewards will outweigh the risks with the possibility of being able to have a far easier and cost effective way to detect cancer and tumors. Being able to use CT and MRI scanners to see the green fluorescent light emitted by the synthetic bacteria makes tumor detection far more accessible for the average person.
VII. Testing
Development and production of the synthetic bacteria is the most critical step of the design. This is the step that will be the most risky and consequential if gone wrong. First, the experiment will be to genetically modify Pseudomonas Aeruginosa, using the top down method and adding the other genes. Additionally, the bacteriostatic agents will be included to make sure that they do not kill the bacteria and that the synthetic bacteria stops reproducing while they are in effect.
The results would provide a sense of the changes needed to be made for the design to work, or precautionary measures that need to be implemented. More extensive testing will provide better insight into synthetic bacterial application for tumor detection.
Quorum Sensing Using Synthetic Bacteria for Detection of Cancerous Tumors
I. Purpose
Cancer is obviously a major issue that our world is facing today. While the mortality rate is slowly decreasing, cancer is not being detected in its early stages when tumors are easier to eliminate. The survival rate in lower stage tumors is drastically higher than in late stage tumors. For example, the survival rate in stage 2 breast cancer is 92%, while the survival rate for stage 4 breast cancer drops drastically to 21%. The reason why cancerous tumors are not being detected in early stages are that they are too expensive for many people to afford. The scanners used are seldom found in the United States, and therefore they are also not accessible to most patients. This issue is important since more people will survival through early detection. The proposed design will solve this issue by making tumor detection more affordable and accessible by optimizing the use of CT and MRI scans which are currently under-utilized.
II. Competing Technologies
The major method of cancer detection is the PET (Positron Emission Tomography) scan. During this scan, the patient is injected with a glucose solution, which contains a minimal amount of radioactive material. Since cancer cells use up more glucose, the PET scan checks for the amount of glucose intake by the cells in the region. The rate at which the glucose is absorbed by tumors is indicative of the stage of the tumor: the faster the rate of glucose absorption, the higher the stage of the tumor. While they are effective in detecting tumors, too much radioactive material can be harmful, and they are also very expensive, often costing nearly $10,000 or more.
III. The Design
Pseudomonas Aeruginosa is a type of gram negative bacteria, which uses quorum sensing for swarm motility, or translocation as a swarm. This bacterium is highly pathogenic and parasitic, and this could lead to major problems. However, with their swarm motility function, it is the perfect bacteria to use for redesigning a chassis. The chassis will be redesigned using the top down method, removing genes repeatedly to find the genes required for to bacteria to survive. Through this process, the parasitic genes will be removed, effectively making the bacteria non-pathogenic. The parasitic genes will be discarded. The genes required for survival, along with the gene for producing receptors for N-AHL (N-acyl Homoserine Lactones, a common signal molecule for gram negative bacteria), a gene for producing N-AHL signal molecules, a gene that allows for binary fission as an asexual reproduction method (this will be in the group of gene required for survival, the GFP (Green Fluorescent Protein) gene, a gene for production of Antigen (Ag) Specific Receptors, and a gene for producing receptors for the major hormone in the organ that is being examined (this is patient-specific and varies from case-to-case).
The genes will be used by a DNA synthesizer to create a genetic code, which will be placed in a synthetic cell. It is also required that antigens will need to be placed on the synthetic bacteria once created since when the bacteria enter the body, the immune system will attack them as foreign cells due to them not having the body’s antigens. Therefore, a blood sample will need to be taken from the patient to extract antigens from red blood cells, which is a very common procedure. The extracted antigen will then bind to the Antigen (Ag) specific receptors on the cell surface.
The Pseudomonas Aeruginosa reproduces by Binary Fission, and therefore by moving the genes for survival of these bacteria, this includes the gene for binary fission, as reproduction is one of the key tenants of life. The rate of reproduction for binary fission is around 20 minutes, so in 12 hours, this can produce about 137.5 billion bacteria. After the bacteria reproduce for about 18 hours, a bacteriostatic agent will be used to stop the synthetic bacteria from reproducing, but without killing them (the specific bacteriostatic agent will have to be found using trial and error, because there is no specific bacteriostatic agent which will work for pseudomonas aeruginosa).
While the bacteriostatic agent is added, a bioinformatics database will be used to compare the genetic codes of the synthetic bacteria with the original code that was created to check for mutations. This is imperative to ensure that mutated bacteria do not enter the body during the tumor detection phase. Pseudomonas Aeruginosa has a high rate of mutation, nearly 67%, so many bacteria will need to be killed off to prevent mutated bacteria from entering the body. Then the bacteriostatic agent will be removed and the non-mutated bacteria will be allowed to reproduce. After many of these cycles, and after approximately 1 trillion bacteria are produced, the bacteria will be injected into the organ where symptoms of cancer are present using a syringe.
In the organ, the bacteria will search for the tumor using quorum sensing for swarm motility (translocation). The synthetic bacteria were given the gene for receptors of a major hormone in the specific organ since changes in major hormone levels can indicate the presence of cancer cells. While the bacteria move through the organ, if they detect a tumor, the gene for GFP will be turned on and the tumor region will fluoresce green. This will allow humans in the outside world to be able to find the tumor location using a MRI or CT scan. If a tumor is not present in the organ, there will not be any green fluorescent color.
While there may not be any cancer in this organ, this does not guarantee that the patient is 100% cancer-free, as the tumor could be located just outside the organ, while the bacteria may not detect this. Therefore, this entire procedure may have to occur multiple times in different locations to make sure that the patient is cancer-free overall. However, the cost of doing many of these tests will still be far less than doing a PET scan.
Synthetic Design Process Flow
Quorum Sensing and Tumor Detection Flow Chart
IV. Expected Results
When the design is working perfectly, all the genes aforementioned will be present and be activated in the minimal bacterial cell, the bacteriostatic agent will completely stop reproduction without killing the bacteria, the bioinformatics database will clearly differentiate between mutated bacteria and non-mutated bacteria, the bacteria will be able to use quorum sensing to move through the organ, and GFP will be activated in the presence of a tumor (if it so exists). The logic switch used will be a buffer gate, with 0 to 0 and 1 to 1 correspondence.
Truth Table
V. Advantages
This design reduces the cost of cancer and tumor detection by nearly 5 times. While there are only a grand total of 62 PET scanner locations in the country, there are thousands of MRI locations, and thousands more CT scanner locations, as these are available at a large amount of hospitals across the country. Two of the five most populous states, New York and Illinois, do not even have PET scanner locations across the entire state. That amounts to over 32 million people who have limited access to cancer detection.
This design is worth funding since it is a solution that makes cancer detection more cost effective and more accessible. This design can save millions of lives of people who are dying of cancer because it is not being detected early enough, which ultimately traces back to affordability.
VI. Potential Problems
If there is a genetic engineering error, this could end up introducing an extremely pathogenic organism into a human, and this would be a very dangerous scenario. Likewise, if the bioinformatics database check is not done to perfection, this could introduce mutated bacteria into the body, and the mutations can be harmful. The bacteriostatic agents must work perfectly to ensure that the bacteria stop reproducing during the bioinformatics database check, while not killing the bacteria. The experiment will need to take place in a very controlled lab environment, to prevent the Pseudomonas Aeruginosa (before it is genetically modified) to infect employees. Also, it is imperative that the mutated synthetic bacteria do not escape the lab environment and cause havoc as these mutations are dangerous. With this design, the rewards will outweigh the risks with the possibility of being able to have a far easier and cost effective way to detect cancer and tumors. Being able to use CT and MRI scanners to see the green fluorescent light emitted by the synthetic bacteria makes tumor detection far more accessible for the average person.
VII. Testing
Development and production of the synthetic bacteria is the most critical step of the design. This is the step that will be the most risky and consequential if gone wrong. First, the experiment will be to genetically modify Pseudomonas Aeruginosa, using the top down method and adding the other genes. Additionally, the bacteriostatic agents will be included to make sure that they do not kill the bacteria and that the synthetic bacteria stops reproducing while they are in effect.
The results would provide a sense of the changes needed to be made for the design to work, or precautionary measures that need to be implemented. More extensive testing will provide better insight into synthetic bacterial application for tumor detection.